arXiv:2605. 21610v2 Announce Type: replace Abstract: Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input.
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2603. 13431v3 Announce Type: replace-cross Abstract: Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development.
arXiv:2607. 20057v1 Announce Type: cross Abstract: Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules.
arXiv:2605. 21600v2 Announce Type: replace Abstract: Computational antibody CDR design methods condition on antigen structure to generate binding loops.
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progress in single-chain protein modeling and generation, they often fall short in antigen-specific antibody design, where effective modeling requires explicit pairing between antibody and antigen, particularly at the epitope level.
arXiv:2606. 28659v1 Announce Type: cross Abstract: High-fidelity molecular docking simulations can produce biologically relevant estimates of epitope-receptor binding affinity but are computationally expensive and therefore limit the number of candidates that can be screened for vaccine design.
arXiv:2607. 18835v1 Announce Type: cross Abstract: Antibodies are essential therapeutic molecules, and their complementarity-determining regions (CDRs) form the primary antigen-recognition interface.
arXiv:2602. 17330v5 Announce Type: replace-cross Abstract: Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority clonotypes.
arXiv:2607. 05846v1 Announce Type: cross Abstract: Accurate ranking of antibody candidates according to their binding affinity is essential for therapeutic antibody discovery.
Accurate ranking of antibody candidates according to their binding affinity is essential for therapeutic antibody discovery. However, existing methods treat affinity comparisons independently and ignore the contextual information encoded in other labeled comparisons, limiting their ability to capture antigen-specific binding landscapes.
arXiv:2606. 02386v1 Announce Type: new Abstract: Protein language models (PLMs) are passive oracles: they generate sequences in a single forward pass with no mechanism to consult external biophysical feedback or redirect generation when a candidate violates thermodynamic or structural constraints.
arXiv:2606. 18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation.